Clone-brush paints with wrong color
An alternate workflow and a much more controlled one is to load your canvas image as a brush texture in the basic TexBrush and use stencil as mapping for the brush - then you can move the image and rotate it exactly how you want it to align, and paint that part into the image.

edit: The Clone brush is mainly meant for cloning pixels to hide the UV seams, and not exactly a way to copy sections of paint onto the canvas without also picking up areas you might not want to pick up - those extra parts usually mean more work to paint out.